Found this... "On the night of April 1 the enemy stormed our upper batteries, defended by a guard of the First Alabama Regiment, and spiked the guns."
OR, Ser. I, Vol. VIII, No. 26, Reports of MacCall, p. 133
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"Yesterday about 1 o'clock a. m. the guns in Battery Numbers 1 were spiked. It was under water and watched by two sentinels, the guard being placed on a breast-height running from the battery to the lake. There was no contest. If not a surprise, the enemy spiked the guns and left before the guard could get in."
Battery Numbers 1, which, under command of Captain Rucker, did such excellent service during the engagement on the 17th instant, will only be fully serviceable again after the water will have fallen. Its guns, spiked by the enemy, are being unspiked. The rat-tail files have been removed out of two of the vents.
(CS) W. W. MACKALL, Brigadier-General, Commanding to Colonel THOMAS JORDAN, Assistant Adjutant-General
HEADQUARTERS, Madrid Bend, April 3, 1862 --- OR
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"Last night an armored boat expedition was fitted out from the squadron and the land forces at this point, under command of Colonel Roberts, of the Forty-second Illinois Regiment. The five boats comprising the expedition were in charge of First Master J. T. Johnson (should read J. V. Johnston), of the Saint Louis, assisted by Fourth Master, G. P. Lord, of the Benton; Fourth Master Pierce, of the Cincinnati; fourth Master Morgan, of the Pittsburgh, and Master's Mate Scoville, of the Mound City, each of the Pittsburg in all 100 men, exclusive of officers, under command of Colonel Roberts.
At midnight the boats reached the upper or Numbers 1 fort, and pulling directly in face, carried it, receiving only the harmless fire of two sentinels, who ran on the discharge of their muskets, while the rebel troops in the vicinity rapidly retreated, whereupon Colonel Roberts spiked the six guns mounted in the fort and retired with the boats uninjured."
OR, Ser. I, Vol. VIII, No. 21, Reports of Flag-Office Andrew H. Foote, U. S. Navy, p.120.
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As far as who was in command of Co. B of the PCA, my educated guess is Capt. William A. Davidson.
Was the "floating battery" and the Upper Battery , i.e., Battery No. 1 the same?
As far as the actual capture of the flag: I agree the facts are unclear. Why would the PCA leave a flag there if the battery was abandoned to the flooding? The flag could have been pilfered from their luggage but the Iverson Batchelor story seems way too credible. Maybe he was attempting to save the flag and he was captured. Also why no mention of the capture of the flag in Union reports? Maybe they wanted to make sure J. V. Johnston got to keep it.
The same exact questions arise when looking at the details of the capture of the PCA flag at Nashville. Can elaborate on that if needed.